GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Corynebacterium deserti GIMN1.010

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_053546028.1 CDES_RS00655 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

Query= curated2:Q9K5Z5
         (515 letters)



>NCBI__GCF_001277995.1:WP_053546028.1
          Length = 1152

 Score =  202 bits (515), Expect = 4e-56
 Identities = 157/497 (31%), Positives = 229/497 (46%), Gaps = 25/497 (5%)

Query: 12  DFSVEENRSAFEAALKNVEGELGKDYPLVINGERVTTDDKIVSVNPAMKEQVIGVVSKAS 71
           D +VEE++   +A L     E   +  L  N E      K  +    +++Q    V    
Sbjct: 464 DRTVEESKELVDAHLHPFANEPDTNPALAQNQEWAELALKRAADPGWLEQQARPDV--VE 521

Query: 72  REIVDDAFKSAETAFHTWKNVNPEERANILIRAAAIIRRRKHEFSAWLVKEAGKPWKEAD 131
            E VD        A   W     EERA IL + A I+  R+    +    E GK  +++D
Sbjct: 522 EEGVDKLIAEVREAALLWAARPAEERARILYKTADILAMRRGHLVSVAAAEVGKSVEQSD 581

Query: 132 ADTAEAIDFLEYYARQMITLKDGKPVNSREGEHNRYFYTPIGVCVTISPWNFALAIMAGT 191
            + +EAIDF  YYA+  + L         +G  N  F TP  + V   PWNF +AI AG+
Sbjct: 582 PEISEAIDFARYYAQLALQL---------DGVDNAEF-TPDRLVVVTPPWNFPIAIPAGS 631

Query: 192 TVAPIVTGNTVLLKPASTTPVVAAKFVEVLEEAGLPKGVVNFVPGSGTDIGDYLIDHPKT 251
           T A +  G  V+ KP+  +   +A  V+ L +AG+P+ V+  V     D G  LI H   
Sbjct: 632 TFAALAAGAGVIHKPSKPSQHCSAAVVQALWDAGVPREVLKCVYPGHRDAGRALISHDLV 691

Query: 252 SLITFTGSRDVGVRLYERAAVVHPGQQHLKRVIVEMGGKDTVVVDKDADLDLAAQSIVTS 311
             +  TGS        E AA+    +  L  +  E  GK+ +V+   AD DLA   +V S
Sbjct: 692 DRVILTGSS-------ETAAMFSSWRPELT-INGETSGKNAIVITPSADRDLAVADLVKS 743

Query: 312 AFGFSGQKCSAGSRAVIHQDVYDV--VLEKAVALTKQLSVGEPTAPDVYMGPVVDQGAFS 369
           AFG +GQKCSA S  ++   VY+      + V     L V  P  P   +GP+ +  +  
Sbjct: 744 AFGHAGQKCSAASLGILVGSVYESERFRRQLVDAASSLIVDWPNNPSATVGPLTELPSDK 803

Query: 370 KIMSYIEVGKEEGRLMVGGEGDDSKGFFIQPTIFADVDPHARIMQEEIFGPVVAFSKARD 429
              +   + + E  L+   + DD+ G    P I   V P       E+FGPV+   +A  
Sbjct: 804 LKHALTTLEEGESWLLEPRQLDDT-GRLWSPGIKDGVSPGTFFHLTEVFGPVLGLMRAET 862

Query: 430 FDHALEIANNTEYGLTGAVITTNRHHIEKAKRDFHVGNLYFNRNCTGAIVGYHPFGGFKM 489
            + A+E+ N  ++GLTG + + +   +        VGN Y NR  TGAIV    FGG+K 
Sbjct: 863 LEEAIELQNGNDFGLTGGLQSLDADEVRTWLDSVDVGNAYVNRGITGAIVQRQSFGGWKK 922

Query: 490 S--GTDSKAGGPDYLAL 504
           S  G  SKAGGP+Y+ L
Sbjct: 923 SSVGLGSKAGGPNYVML 939


Lambda     K      H
   0.318    0.135    0.394 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1211
Number of extensions: 45
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 515
Length of database: 1152
Length adjustment: 41
Effective length of query: 474
Effective length of database: 1111
Effective search space:   526614
Effective search space used:   526614
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory